I am seeking to get married. My family spoke with another family and I spoke with their daughter. They seemed like a good family and we all liked each other.

I felt I was for the most part compatible with the girl, but I still was not sure so I did a 2 rakat prayer for Allah to help with my decision. I was still confused and prayed another 2 rakat prayer a couple of days later. In the end we did istikhara of Quran from a Sheikh and he said the istikhara was not good and that it would cause a lot of problems.

I heard of some people who do istikhara multiple times. Does it make sense to do this? What would you advise in my situation?

The istikhra is seeking advice from Allah swt.
Going against is not forbidden however unpleasant consequences happen as many has experienced.
But if there is a sense that circumstances have changed or something has changed in the matter then one can retake the istikhra